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  <p align="center" class="style2"><strong>miGLE Guide</strong><br>
    <span class="style3">(Version 1.0</span><span class="style3">) </span> </p>
  <p class="style1">Introduction</p>
  <p class="style3">The framewrok of this server is shown in Fig. 1. </p>
  <p align="center" class="style3"><img src="graphs/migleFramework.jpg" width="480" height="435"></p>
  <p align="center" class="style3">Fig. 1 Framework of miGLE</p>
  <p align="center" class="style3">&nbsp; </p>
  <p class="style1">Input Sequence</p>
  <p class="style3">For bioinformatics analysis of mutation in 3' UTR, there is two approaches. One is start from mutation sequence and wild sequence; another approach start only from wild sequence and get mutation sequence by simulation. When consider point mutaion, the latter is matter for user. </p>
  <p class="style1">microRNA:target Interaction analysis</p>
  <p class="style1">&nbsp;</p>
  <p align="left"><span class="style1">Results</span></p>
  <p align="left">Firstly, you will get the gain and loss events of miRNA-target interaction(GLEs). The red bar stand for the number of gain-target and the green bar stands for the number of loss-target. The number is computed by the sum of target-gain and target-loss for each microRNA.</p>
  <p align="left">Secondly, you can click each bar to see the detail. Click here for a <a href="graphs/migle.gif">screen shot</a> of resutls.</p>
  <p align="left">After click, a new window will pop up. You can see the details of target-loss or target-gain. For the abbreviation, please click <a href="graphs/singleInfo.jpg">here</a>. </p>
  <p align="left">According microRNA target background, the relationship of mutant locus with background target region and the new target region, we classify the mutation into eight types. Click <a href="graphs/classification.gif">here</a> for the detail.</p>
  <p class="style1">Coding System for 3' UTR</p>
  <p>We have three coding system for the locating interested region in 3' UTR. This coding system can be set by user by rearrange two parameters: start codon position and the last nucelotide for coding regions.The details is shown below. If the input file is in fata format. The user should compile the sequence as following. For fasta input, the first nucleotide is counted as 1. </p>
  <p align="center">Table 1 Coding System used by miGLE </p>
  <table width="880" border="1">
    <tr>
      <td width="20" height="47">&nbsp;</td>
      <td width="47">Start Codon </td>
      <td width="114">First Nucleotide</td>
      <td width="380"><div align="center">Standard Expression </div></td>
      <td width="285">Description</td>
    </tr>
    <tr>
      <td height="56">1</td>
      <td>1</td>
      <td>x</td>
      <td>&gt;122939142|miGLE|StartCodon|1|Cds_Length|1080<br>
      </td>
      <td>Counting from translation start codon(This is prefered by miGLE). If this coding system is adapted, then the 3' UTR start from 1081. </td>
    </tr>
    <tr>
      <td>2</td>
      <td>0</td>
      <td>0</td>
      <td>&gt;122939142|miGLE|StartCodon|0|Cds_Length|0</td>
      <td><p>counting from the first 3' UTR nucleotide.This is a default coding system for fasta input. <br>
        If this coding system is adapted, then 3' UTR start from 1. </p>
      </td>
    </tr>
    <tr>
      <td>3</td>
      <td>x</td>
      <td>x</td>
      <td>&gt;122939142|miGLE|StartCodon|389|Cds_Length|1080</td>
      <td>Counting from transcription start point.<br>
      This coding system is not stable.It should not be used as far as possible. </td>
    </tr>
  </table>
  <p>* for FASTA file Only. The genbank file will adopt the type 1 coding system. </p>
  <p align="left"><span class="style1">Contact us </span></p>
  <p align="left">For any suggestion please contact with Zuofeng Li at zfli@scbit.org.</p>
  <p align="left"> Zuofeng Li<br>
    Floor 12, Building 1,<br>
    No. 100 Qinzhou Road,<br>
    Shanghai, China, 200235</p>
  <hr>
  <div align="center">
    <p>Biomedical Informatics Research Group <br>
      Shanghai Center 
    for Bioinformation Technology<br>
    2007.12
    <br>
    </p>
  </div>
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